Variant report

Variant	rs1653588
Chromosome Location	chr12:121676666-121676667
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121660603..121665110-chr12:121671733..121676729,4	K562	blood:
2	chr12:121666865..121669227-chr12:121676180..121679076,2	MCF-7	breast:
3	chr12:121673925..121677209-chr12:121686132..121689078,3	MCF-7	breast:
4	chr12:121676166..121678548-chr12:121679208..121682170,2	K562	blood:
5	chr12:121668796..121670934-chr12:121675457..121678613,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1169716	0.82[AFR][1000 genomes]
rs1169719	1.00[YRI][hapmap]
rs1169721	0.88[CHB][hapmap]
rs1169723	1.00[YRI][hapmap]
rs1169810	1.00[YRI][hapmap]
rs1186053	1.00[YRI][hapmap]
rs1630178	1.00[YRI][hapmap]
rs1653586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653592	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1653593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1653599	0.82[AFR][1000 genomes]
rs1718118	0.86[EUR][1000 genomes]
rs1718156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718157	0.82[AFR][1000 genomes]
rs1718158	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975123	0.87[YRI][hapmap]
rs2071272	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs208297	0.83[YRI][hapmap]
rs2252298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2252304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2288691	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2288693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs25642	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2567982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2567983	0.83[YRI][hapmap]
rs2567998	0.87[YRI][hapmap]
rs2668239	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2668246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2686339	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2686381	0.87[YRI][hapmap]
rs2686392	0.83[ASN][1000 genomes]
rs28969487	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815990	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57379013	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57419819	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57983015	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59037892	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60714133	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60979871	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv899564	chr12:121641509-121689798	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899565	chr12:121641509-121698785	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv455731	chr12:121668254-121687174	Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv560456	chr12:121668254-121687174	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121649400-121680200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:121653200-121698800	Weak transcription	Fetal Heart	heart
3	chr12:121653400-121677600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:121653400-121678600	Weak transcription	Right Atrium	heart
5	chr12:121655200-121678000	Weak transcription	Fetal Kidney	kidney
6	chr12:121662000-121676800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:121662000-121679000	Weak transcription	K562	blood
8	chr12:121662800-121690600	Weak transcription	Fetal Brain Male	brain
9	chr12:121665600-121681400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:121665800-121678600	Weak transcription	NH-A	brain
11	chr12:121666000-121676800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:121666600-121679200	Strong transcription	Lung	lung
13	chr12:121667000-121678000	Weak transcription	Left Ventricle	heart
14	chr12:121667600-121676800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:121667800-121685200	Weak transcription	Hela-S3	cervix
16	chr12:121668400-121677400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:121668600-121678400	Weak transcription	A549	lung
18	chr12:121668600-121678400	Weak transcription	HepG2	liver
19	chr12:121669800-121677800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr12:121669800-121678000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:121670200-121689400	Strong transcription	Fetal Brain Female	brain
22	chr12:121670600-121695000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:121671000-121678000	Weak transcription	NHDF-Ad	bronchial
24	chr12:121671200-121686200	Weak transcription	Small Intestine	intestine
25	chr12:121671400-121676800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:121671800-121681200	Weak transcription	Brain Angular Gyrus	brain
27	chr12:121672200-121678800	Weak transcription	HSMM	muscle
28	chr12:121672800-121679200	Weak transcription	Ovary	ovary
29	chr12:121673000-121677800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:121673200-121679800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:121673600-121677800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:121673600-121678000	Weak transcription	Aorta	Aorta
33	chr12:121673600-121678400	Genic enhancers	Fetal Intestine Large	intestine
34	chr12:121673600-121679600	Strong transcription	Dnd41	blood
35	chr12:121673600-121681200	Weak transcription	HMEC	breast
36	chr12:121673800-121677200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:121673800-121678200	Genic enhancers	Fetal Intestine Small	intestine
38	chr12:121674400-121678200	Weak transcription	NHLF	lung
39	chr12:121674400-121687800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:121674600-121677200	Enhancers	Pancreas	Pancrea
41	chr12:121674600-121678200	Genic enhancers	Liver	Liver
42	chr12:121674600-121692800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:121674600-121704200	Strong transcription	Brain Germinal Matrix	brain
44	chr12:121674800-121676800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:121675000-121676800	Weak transcription	Esophagus	oesophagus
46	chr12:121675200-121677400	Genic enhancers	HUVEC	blood vessel
47	chr12:121675200-121678400	Genic enhancers	Fetal Stomach	stomach
48	chr12:121675400-121677000	Genic enhancers	Brain Cingulate Gyrus	brain
49	chr12:121675400-121678000	Enhancers	Colon Smooth Muscle	Colon
50	chr12:121675400-121678400	Strong transcription	Colonic Mucosa	Colon

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